From 76336a2d8cb0714f690d81623dafc284907c502b Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 3 Jul 2023 12:47:55 -0600 Subject: [PATCH] Address CMD check doc complaints, update NAMESPACE and bump pkg version --- DESCRIPTION | 2 +- NAMESPACE | 5 +++++ R/datasets.R | 5 +++-- man/add_to_collection.Rd | 2 +- man/nf_sarek_datasets.Rd | 2 ++ man/use_latest_in_collection.Rd | 2 +- 6 files changed, 13 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b4e735c1..5cd8e93c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: nfportalutils Title: NF Portal Utilities -Version: 0.0.0.9210 +Version: 0.0.0.9300 Authors@R: c( person(given = "Robert", family = "Allaway", role = c("aut", "cre"), email = "robert.allaway@sagebionetworks.org", diff --git a/NAMESPACE b/NAMESPACE index 6c68ffc5..c739fdbd 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -16,6 +16,7 @@ export(add_people_from_table) export(add_publication_from_pubmed) export(add_publication_from_unpaywall) export(add_publications_from_file) +export(add_to_collection) export(annotate_aligned_reads) export(annotate_called_variants) export(annotate_expression) @@ -49,7 +50,10 @@ export(map_sample_io) export(map_sample_output_rnaseq) export(map_sample_output_sarek) export(missing_annotation_email) +export(new_dataset) export(new_project) +export(nf_sarek_datasets) +export(nf_star_salmon_datasets) export(processing_flowchart) export(qc_manifest) export(register_study) @@ -61,6 +65,7 @@ export(syn_login) export(syncBP_maf) export(table_query) export(update_study_annotations) +export(use_latest_in_collection) export(wiki_mod) import(data.table) import(reticulate) diff --git a/R/datasets.R b/R/datasets.R index 164263b2..1cb41b07 100644 --- a/R/datasets.R +++ b/R/datasets.R @@ -52,7 +52,7 @@ update_items <- function(current_coll, update_coll) { #' Update an _existing_ collection so that all items or a subset of items reference their latest version. #' This should work for both datasets (collection of files) and dataset collections (collection of datasets). #' -#' @param collection_id +#' @param collection_id Collection id. #' @param items Vector of dataset ids for which to update reference to latest version, #' or "all" (default) to update all in the dataset collection. #' @export @@ -93,7 +93,7 @@ use_latest_in_collection <- function(collection_id, items = "all") { #' Thus, while this is generic enough to handle both datasets and dataset collections #' it is expected to be used more for dataset collections given that the dataset method is provided. #' -#' @param collection_id Id of the collection. +#' @param collection_id Collection id. #' @param items Character vector of one or more dataset entity ids to add. #' @param check_items Whether to check that ids are really appropriate item types and remove non-appropriate item types #' to help avoid Synapse errors (default `FALSE` because in most cases `items` are curated, and using check will be slower). @@ -171,6 +171,7 @@ new_dataset <- function(name, parent, items, item_version = NULL, dry_run = TRUE #' #' @inheritParams new_dataset #' @param output_map The `data.table` returned from `map_sample_output_sarek`. See details for alternatives. +#' @param workflow One of workflows used. #' @param verbose Optional, whether to be verbose -- defaults to TRUE. #' @import data.table #' @return A list of dataset objects. diff --git a/man/add_to_collection.Rd b/man/add_to_collection.Rd index e6d774a4..0b52c9e6 100644 --- a/man/add_to_collection.Rd +++ b/man/add_to_collection.Rd @@ -7,7 +7,7 @@ add_to_collection(collection_id, items, check_items = FALSE, force = FALSE) } \arguments{ -\item{collection_id}{Id of the collection.} +\item{collection_id}{Collection id.} \item{items}{Character vector of one or more dataset entity ids to add.} diff --git a/man/nf_sarek_datasets.Rd b/man/nf_sarek_datasets.Rd index db4012d6..46ddbe61 100644 --- a/man/nf_sarek_datasets.Rd +++ b/man/nf_sarek_datasets.Rd @@ -17,6 +17,8 @@ nf_sarek_datasets( \item{parent}{Synapse id of parent project where the dataset will live.} +\item{workflow}{One of workflows used.} + \item{verbose}{Optional, whether to be verbose -- defaults to TRUE.} \item{dry_run}{If TRUE, don't actually store dataset, just return the data object for inspection or further modification.} diff --git a/man/use_latest_in_collection.Rd b/man/use_latest_in_collection.Rd index 00c376d9..8a8983d3 100644 --- a/man/use_latest_in_collection.Rd +++ b/man/use_latest_in_collection.Rd @@ -7,7 +7,7 @@ use_latest_in_collection(collection_id, items = "all") } \arguments{ -\item{collection_id}{} +\item{collection_id}{Collection id.} \item{items}{Vector of dataset ids for which to update reference to latest version, or "all" (default) to update all in the dataset collection.}